The evil mad scientist Dr. Eggman is up to his old nasty tricks again.

"Sonic…that annoying, impertinent hedgehog. Thanks to him, my great plans are always laid to waste! Oh, but this time, I'm going to rub him out with the power of science! Ha ha ha ha ha…"

South Island is a treasure trove of gems and ancient ruins. They say that it's the island where the mystical Chaos Emeralds lie. The Chaos Emeralds are a super-material that give energy to all living beings. Also, when applied to scientific purposes, they can be used for nuclear and laser based weaponry. However, nobody knows exactly how to get ahold of these emeralds. At the same time, though, they do say that the reason why South Island is always moving is because the emeralds are somewhere inside the island's hazy depths.

One day, crisis visited upon the island. And who showed up with it but Dr. Eggman and his cronies.

"I'll find those emeralds even if I have to dig up the entire island to do it!"

Dr. Eggman set up a fort in one corner of the island, and went about carrying out his plan.

"Eggman, you still haven't had enough?"

Sonic hurried as soon as he heard the news. Dr. Eggman never seemed to leave him alone, even though Sonic had beaten him every time so far. It sounded like Dr. Eggman considered Sonic his sworn enemy, but he was never any match for Sonic.

However, this time something is amiss.

"Have you seen it, Sonic? This time is going to be different! Because this time, I've turned all the animals on the island into robots!"

"E...Everybody!?"

"All of them go about in accordance to my orders. In other words, Sonic, everyone on the island is your enemy! Gya— Ha ha ha ha ha ha ^cough^ ^ack^ ^ahem^. This time, the world really will be all mine!"

This is terrible! Hurry! Sonic the Hedgehog - everyone is waiting for your help!

At the end of Sonic the Hedgehog, Dr. Robotnik's Scrap Brain facility was destroyed, but the evil doctor narrowly escaped.

Now Robotnik is back and plans to conquer the world once more. He secretly follows Sonic's biplane, the Tornado, to his vacation spot, West Side Island. According to legend, an ancient civilization once abused the power of seven Chaos Emeralds on West Side Island. Sonic meets a peculiar two-tailed fox named Miles Prower, better known as "Tails". The two become good friends. Meanwhile, Robotnik begins his search for the Chaos Emeralds to fuel his new Death Egg warship. One afternoon, he launches his full-scale attack on the island. He imprisons all of the animals of the island and turns them into mindless worker drones called Badniks. Fortunately, Sonic is determined to thwart the Doctor at all costs. This time, he isn't alone, as Tails decides to aid him. Together they must locate the Emeralds before Robotnik does, and stop him before the Death Egg is complete.